Endogenous pigments are substances in living matter that absorb visible light. They may also absorb UV radiation. These substances are produced either within tissues and serve a physiological function, or they are by-products of the metabolic process. Endogenous pigments can be classified into non-hematogenous pigments and hematogenous (i.e., blood derived) pigments. Non-hematogenous pigments include, e.g., melanins, flavins, pterins, and urocanic acid. Melanins are derived from tyrosine, and include eumelaninm pheomelanin, and neuromelanin. Flavins are a group of organic compounds based on pteridine, formed by the tricyclic heteronuclear organic ring isoalloxazine. Examples of flavins include riboflavin, flavin mononucleotide, flavoproteins, and flavin adenine dinucleotide. Pterins are heterocyclic compounds composed of a pteridine ring system, with a keto group and an amino group on positions, 4 and 2, respectively. Examples of pterins include pteridine, biopterin, tetrahydrobiopterin, molybdopterin, cyanopterin, tetrahydromethanopterin, and folic acid. Urocanic acid is an intermediate in the catabolism of L-histidine. Hematogenous pigments include, e.g., hemoglobin, bile pigments, and porphyrins. Hemoglobin is a basic, conjugated protein that is responsible for the transportation of oxygen and carbon dioxide within the blood stream. It is composed of protein, globin, and heme-four molecules of heme are attached to each molecule of globin.

Heme B group of hemoglobin complexed to four interior nitrogen atoms Bile pigments are the metabolic products of heme, and include bilirubin (yellow, tetrapyrrolic breakdown product) and biliverdin (green, tetrapyrrolic breakdown product).
Porphyrins are a group of organic compounds, mainly naturally occurring, but also can be exogenous. Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at their a carbon atoms via methine bridges (═CH—), as shown in Formula (I). Porphyrins are aromatic. That is, they obey Hickel's rule for aromaticity, possessing 4n+2π electrons (n=4 for the shortest cyclic path) delocalized over the macrocycle. Thus, porphyrin macrocycles are highly conjugated systems and typically have very intense absorption bands in the visible region and may be deeply colored. The macrocycle has 26 π electrons in total. The parent porphyrin is porphine, and substituted porphines are called porphyrins. The porphyrin compounds that have their singlet and triplet excited states quenched by the conjugated, fused tricyclic compound having electron withdrawing groups include any porphyrin compound that includes the moiety of Formula (I) (and derivatives and tautomers thereof), as shown in Formula Ia, particularly protoporphyrin IX, Formula Ib.

A porphyrin without a metal-ion in its cavity is a free base. Some iron-containing porphyrins are called hemes, the pigment in red blood cells. As previously discussed, heme is a cofactor of the protein hemoglobin. Heme-containing proteins, or hemoproteins, are found extensively in nature. Hemoglobin and myoglobin are two O2-binding proteins that contain iron porphyrins. Various cytochromes are also hemoproteins.
The absorption of visible light (at about 400 to about 800 nm and UV of about 290 to about 400 nm) by a porphyrin compound causes the excitation of an electron in the porphyrin molecule from an initially occupied, lower energy orbital to a higher energy, previously unoccupied orbital. The energy of the absorbed photon is used to energize an electron and cause it to “jump” to a higher energy orbital. See Turro, Modern Molecular Photochemistry, 1991. Two excited electronic states derive from the electronic orbital configuration produced by visible light absorption. In one state, the electron spins are paired (antiparallel) and in the other state the electron spins are unpaired (parallel). The state with paired spins has no resultant spin magnetic moment, but the state with unpaired spins possesses a net spin magnetic moment. A state with paired spins remains a single state in the presence of a magnetic field, and is termed a singlet state. A state with unpaired spins interacts with a magnetic field and splits into three quantized states, and is termed a triplet state.
In the electronically excited state, the porphyrin molecule can transfer its excited state energy to oxygen contained in blood and/or skin cells, thereby generating cell-damaging singlet excited state oxygen (hereinafter “singlet oxygen”), or free radical oxygen. To photostabilize the excited state of the porphyrin molecule so that it does not generate cell-toxic singlet oxygen, the excited state of the porphyrin molecule must be returned to the ground state before it transfers its excited state energy to nearby oxygen molecule.
On the other hand, the excited state of porphyrins has also been intentionally harnassed to administer photodynamic therapy (PDT). Protoporphyrin IX (C34H34N4O4) is used in PDT, for example, as a treatment for basal cell carcinoma (BCC), which is the most common form of skin cancer in humans. The PDT treatment involves applying a photosensitizer precursor, such as aminolevulinic acid (ALA) to the cancerous cells, waiting a few hours for the ALA to be taken up by the cells and converted to protoporphyrin IX, and then irradiating the cancerous cells with light in the wavelength of about 380 to about 650 nm which excites the protoporphyrin IX to a singlet excited state after which it intersystem crosses to a triplet excited state thereby making it reactive with oxygen, thereby generating cytotoxic singlet oxygen that kills cancerous and pre-cancerous cells.